Contacts of the helix formed by residues 37 - 47 (chain O) in PDB entry 3K9Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 37 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O THR* 1.3 82.8 + - - +
38O ASP* 1.3 64.1 + - - +
39O ASP* 3.6 14.9 - - - +
40O MET* 3.1 23.4 + - - +
41O LEU* 3.1 24.5 + - - +
194R GLY* 6.1 1.4 - - - -
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Residues in contact with ASP 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ASP* 1.3 73.1 - - - +
39O ASP* 1.3 68.4 + - - +
41O LEU* 3.2 8.5 + - - +
42O ALA* 2.8 28.1 + - - +
60O VAL* 3.8 22.3 - - + +
61O VAL 4.4 3.3 - - - +
63O GLY* 4.2 3.6 + - - -
64O GLY* 3.5 28.3 + - - +
65O PHE* 4.1 3.8 - - + -
74O SER* 2.4 35.4 + - - -
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Residues in contact with ASP 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ASP* 3.6 15.4 - - - +
38O ASP* 1.3 77.5 - - - +
40O MET* 1.3 61.9 + - - +
42O ALA* 4.0 2.1 - - - +
43O HIS* 3.2 24.3 + - - +
60O VAL* 4.1 15.8 - - + +
194R GLY 5.2 1.2 - - - +
196R LYS* 2.7 41.0 + - - +
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Residues in contact with MET 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O THR* 3.3 32.3 - - + +
37O ASP* 3.1 8.8 + - - +
39O ASP* 1.3 78.0 + - - +
41O LEU* 1.3 59.5 + - - +
43O HIS* 3.2 5.6 + - - +
44O LEU* 3.0 57.8 + - + +
190R PRO* 4.0 4.7 - - + -
191R HIS 4.1 12.6 - - - +
194R GLY* 3.6 39.9 - - - +
195R ASP 4.0 8.1 - - - +
196R LYS* 3.9 19.7 - - + -
199R ALA* 3.9 15.0 - - - -
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Residues in contact with LEU 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PHE* 3.7 38.1 - - + +
32O VAL* 4.1 14.1 - - + -
34O ASP* 4.1 11.9 - - + -
36O THR* 3.6 25.4 - - + +
37O ASP 3.1 15.4 + - - +
38O ASP* 3.2 12.3 + - - +
40O MET* 1.3 76.5 - - + +
42O ALA* 1.3 62.3 + - - +
44O LEU* 3.3 4.8 + - + +
45O LEU* 3.0 23.2 + - - +
65O PHE* 4.1 13.2 - - + -
74O SER* 4.0 26.2 - - - +
75O PHE 5.2 4.0 - - - +
190R PRO* 5.3 2.5 - - + -
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Residues in contact with ALA 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ASP 2.8 19.1 + - - +
39O ASP 4.0 2.2 - - - +
41O LEU* 1.3 72.1 - - - +
43O HIS* 1.3 56.8 + - - +
45O LEU* 3.2 6.7 + - - +
46O LYS* 2.9 39.2 + - + +
58O VAL* 3.8 25.7 - - + +
60O VAL* 3.8 22.7 - - + +
65O PHE* 4.7 11.5 - - + -
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Residues in contact with HIS 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ASP 3.2 17.0 + - - +
40O MET* 3.5 5.6 - - - +
41O LEU 3.2 0.2 - - - -
42O ALA* 1.3 79.9 - - - +
44O LEU* 1.3 68.2 + - + +
46O LYS* 3.2 12.6 + - - +
47O TYR* 3.0 58.5 + + + +
276Q ASP* 4.8 1.9 - - + +
277Q GLU* 3.4 39.6 + - - -
196R LYS* 3.7 46.1 + - + +
200R ARG* 4.2 10.7 + - - -
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Residues in contact with LEU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PHE 5.6 0.4 - - - +
15O ARG* 3.1 37.0 + - - +
19O ARG* 4.8 2.1 + - - -
40O MET* 3.0 35.1 + - + +
41O LEU* 4.1 3.6 - - + +
43O HIS* 1.3 79.7 - - + +
45O LEU* 1.3 62.9 + - - +
47O TYR 3.0 18.5 - - - +
48O ASP* 4.8 2.3 - - - +
188R ASP* 4.3 15.5 - - + -
189R ALA* 3.5 35.0 - - - +
190R PRO* 3.6 10.3 - - + -
199R ALA* 4.4 8.7 - - + -
200R ARG* 4.0 27.1 - - - +
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Residues in contact with LEU 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PHE* 4.1 11.4 - - + -
15O ARG* 3.8 11.3 - - + +
18O PHE* 3.7 38.1 - - + -
19O ARG* 3.0 34.0 + - + +
41O LEU 3.0 14.0 + - - +
42O ALA 3.5 6.1 - - - +
44O LEU* 1.3 78.1 - - - +
46O LYS* 1.3 62.2 + - - +
54O PHE* 3.3 27.0 - - + +
58O VAL* 3.9 27.1 - - + -
65O PHE* 4.0 22.9 - - + -
67O VAL* 4.0 3.1 - - + -
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Residues in contact with LYS 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ALA* 2.9 31.2 + - + +
43O HIS* 3.2 11.1 + - - +
45O LEU* 1.3 71.8 - - - +
47O TYR* 1.3 81.2 + - + +
53O ARG* 3.4 6.4 - - - +
54O PHE* 2.8 35.5 + - + +
56O GLY 5.7 2.5 - - - +
58O VAL* 3.9 38.0 + - + +
276Q ASP* 3.3 35.2 + - - -
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Residues in contact with TYR 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O ARG* 5.5 0.2 + - - -
43O HIS* 3.0 41.6 + + + +
44O LEU* 3.0 24.4 - - - +
46O LYS* 1.3 100.9 - - + +
48O ASP* 1.3 60.4 + - - +
53O ARG* 3.6 33.2 + - + +
274Q THR* 4.8 1.7 + - - -
276Q ASP* 2.6 33.0 + - - +
278Q ILE* 3.5 22.0 - - + +
282Q ASP* 3.2 32.5 - - + +
188R ASP* 4.1 5.2 - - - +
200R ARG* 3.5 18.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il